Align Methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial; MMSDH; Malonate-semialdehyde dehydrogenase [acylating]; Aldehyde dehydrogenase family 6 member A1; EC 1.2.1.18; EC 1.2.1.27 (characterized)
to candidate Pf6N2E2_1309 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase (EC 1.2.1.60)
Query= SwissProt::Q02253 (535 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1309 Length = 486 Score = 218 bits (555), Expect = 4e-61 Identities = 141/440 (32%), Positives = 230/440 (52%), Gaps = 13/440 (2%) Query: 40 VKLFIDGKFVESKSDKWIDIHNPATNEVVGRVPQSTKAEMEAAVAACKRAFPAWADTSIL 99 +K +IDG+ VESK D +++ +NPAT E +G V E+ AVAA K AFP WA+T Sbjct: 2 IKHWIDGREVESK-DVFVN-YNPATGEAIGEVASGGAEEVAQAVAAAKEAFPKWANTPAK 59 Query: 100 SRQQVLLRYQQLIKENLKEIARLITLEQGKTLADAEGDVF-RGLQVVEHACSVTSLMLGE 158 R +++ + +LI++N+ ++A L TL+ G + + + R + V + M G Sbjct: 60 ERARLMRKLGELIEQNVPQLAELETLDTGLPIHQTKNVLIPRASHNFDFFAEVCTRMDGH 119 Query: 159 TMPSITKDMDLYSYRLPLGVCAGIAPFNFPAMIPLWMFPMAMVCGNTFLMKPSERVPGAT 218 T P + M Y+ P+GVCA ++P+N P M W + GNT ++K SE P Sbjct: 120 TYP-VDDQMLNYTLYQPVGVCALVSPWNVPFMTATWKTAPCLALGNTAVLKMSELSPLTA 178 Query: 219 MLLAKLLQDSGAPDGTLNIIHGQ-HEAVNFICDHPDIKAISFVGSNQAGEYIFERGSRNG 277 L +L ++G P+G LN+I G A + + HPD++AISF G G+ I + Sbjct: 179 NELGRLAVEAGIPNGVLNVIQGYGATAGDALVRHPDVRAISFTGGTATGKKIMQTAGL-- 236 Query: 278 KRVQANMGAKNHGVVMPDANKENTLNQLVGAAFGAAGQRCMALSTAVLVGEA--KKWLPE 335 K+ +G K+ ++ DA+ E L+ + F G+RC A + + + E+ +++ E Sbjct: 237 KKYSMELGGKSPVLIFEDADLERALDAALFTIFSLNGERCTA-GSRIFIQESVYPQFVAE 295 Query: 336 LVERAKNLRVNAGDQPGADLGPLITPQAKERVCNLIDSGAKEGASILLDG--RKIKVKGY 393 RAK L V P +G +IT ++V I G +EGA++L G R + + Sbjct: 296 FAARAKRLIVGDPQDPKTQVGSMITQAHYDKVTGYIKIGLEEGATLLAGGLERPANLPAH 355 Query: 394 -ENGNFVGPTIISNVKPSMTCYKEEIFGPVLVVLETETLDEAIKIVNDNPYGNGTAIFTT 452 G F+ PT+ ++V M +EEIFGPV+ ++ + EA+ + ND YG + I+T Sbjct: 356 LSRGQFIQPTVFADVNNKMRIAQEEIFGPVVCLIPFKDEAEALHLANDTEYGLASYIWTQ 415 Query: 453 NGAIARKYAHMVDVGQVGVN 472 + A + AH ++ G V +N Sbjct: 416 DIGKAHRLAHGIEAGMVFIN 435 Lambda K H 0.318 0.133 0.389 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 526 Number of extensions: 26 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 535 Length of database: 486 Length adjustment: 34 Effective length of query: 501 Effective length of database: 452 Effective search space: 226452 Effective search space used: 226452 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory